Mercurial > repos > devteam > kraken_report
changeset 0:f2757ab26483 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author | devteam |
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date | Thu, 23 Jul 2015 10:56:14 -0400 |
parents | |
children | 688428f6800f |
files | README.rst kraken-mpa-report.xml kraken-report.xml macros.xml tool-data/kraken_databases.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
diffstat | 6 files changed, 256 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Jul 23 10:56:14 2015 -0400 @@ -0,0 +1,92 @@ +Introduction +============ + +`Kraken <http://ccb.jhu.edu/software/kraken/>`__ is a taxonomic sequence +classifier that assigns taxonomic labels to short DNA reads. It does +this by examining the :math:`k`-mers within a read and querying a +database with those :math:`k`-mers. This database contains a mapping of +every :math:`k`-mer in +`Kraken <http://ccb.jhu.edu/software/kraken/>`__'s genomic library to +the lowest common ancestor (LCA) in a taxonomic tree of all genomes that +contain that :math:`k`-mer. The set of LCA taxa that correspond to the +:math:`k`-mers in a read are then analyzed to create a single taxonomic +label for the read; this label can be any of the nodes in the taxonomic +tree. `Kraken <http://ccb.jhu.edu/software/kraken/>`__ is designed to be +rapid, sensitive, and highly precise. Our tests on various real and +simulated data have shown +`Kraken <http://ccb.jhu.edu/software/kraken/>`__ to have sensitivity +slightly lower than Megablast with precision being slightly higher. On a +set of simulated 100 bp reads, +`Kraken <http://ccb.jhu.edu/software/kraken/>`__ processed over 1.3 +million reads per minute on a single core in normal operation, and over +4.1 million reads per minute in quick operation. + +The latest released version of Kraken will be available at the `Kraken +website <http://ccb.jhu.edu/software/kraken/>`__, and the latest updates +to the Kraken source code are available at the `Kraken GitHub +repository <https://github.com/DerrickWood/kraken>`__. + +If you use `Kraken <http://ccb.jhu.edu/software/kraken/>`__ in your +research, please cite the `Kraken +paper <http://genomebiology.com/2014/15/3/R46>`__. Thank you! + +System Requirements +=================== + +Note: Users concerned about the disk or memory requirements should read +the paragraph about MiniKraken, below. + +- **Disk space**: Construction of Kraken's standard database will + require at least 160 GB of disk space. Customized databases may + require more or less space. Disk space used is linearly proportional + to the number of distinct :math:`k`-mers; as of Feb. 2015, Kraken's + default database contains just under 6 billion (6e9) distinct + :math:`k`-mers. + + In addition, the disk used to store the database should be + locally-attached storage. Storing the database on a network + filesystem (NFS) partition can cause Kraken's operation to be very + slow, or to be stopped completely. As NFS accesses are much slower + than local disk accesses, both preloading and database building will + be slowed by use of NFS. + +- **Memory**: To run efficiently, Kraken requires enough free memory to + hold the database in RAM. While this can be accomplished using a + ramdisk, Kraken supplies a utility for loading the database into RAM + via the OS cache. The default database size is 75 GB (as of Feb. + 2015), and so you will need at least that much RAM if you want to + build or run with the default database. + +- **Dependencies**: Kraken currently makes extensive use of Linux + utilities such as sed, find, and wget. Many scripts are written using + the Bash shell, and the main scripts are written using Perl. Core + programs needed to build the database and run the classifier are + written in C++, and need to be compiled using g++. Multithreading is + handled using OpenMP. Downloads of NCBI data are performed by wget + and in some cases, by rsync. Most Linux systems that have any sort of + development package installed will have all of the above listed + programs and libraries available. + + Finally, if you want to build your own database, you will need to + install the + `Jellyfish <http://www.cbcb.umd.edu/software/jellyfish/>`__ + :math:`k`-mer counter. Note that Kraken only supports use of + Jellyfish version 1. Jellyfish version 2 is not yet compatible with + Kraken. + +- **Network connectivity**: Kraken's standard database build and + download commands expect unfettered FTP and rsync access to the NCBI + FTP server. If you're working behind a proxy, you may need to set + certain environment variables (such as ``ftp_proxy`` or + ``RSYNC_PROXY``) in order to get these commands to work properly. + +- **MiniKraken**: To allow users with low-memory computing environments + to use Kraken, we supply a reduced standard database that can be + downloaded from the Kraken web site. When Kraken is run with a + reduced database, we call it MiniKraken. + + The database we make available is only 4 GB in size, and should run + well on computers with as little as 8 GB of RAM. Disk space required + for this database is also only 4 GB. + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kraken-mpa-report.xml Thu Jul 23 10:56:14 2015 -0400 @@ -0,0 +1,71 @@ +<tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.1.0"> + <expand macro="version_command" /> + <expand macro="requirements" /> + <expand macro="stdio" /> + <description> + view report of classification for multiple samples + </description> + <macros> + <import>macros.xml</import> + </macros> + <command> + <![CDATA[ + +#for $input_count, $input_classification in enumerate( $classification ): + ln -s "${input_classification}" "sample_${input_count}" && +#end for + +kraken-mpa-report @INPUT_DATABASE@ + +#for $input_count, $input_classification in enumerate( $classification ): + "sample_${input_count}" +#end for + +${show_zeros} +${header_line} + +> "$output_report" + + + ]]> + </command> + <inputs> + <param multiple="True" name="classification" type="data" format="tabular" label="Kraken output"/> + <param name="show_zeros" type="boolean" truevalue="--show-zeros" falsevalue="" checked="False" label="Display taxa even if they lack a read in any sample" help="--show-zeros"/> + <param name="header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="False" label="Display a header line indicating sample IDs" help="--header-line"/> + <expand macro="input_database" /> + </inputs> + <outputs> + <data format="tabular" name="output_report" /> + </outputs> + <help> +<![CDATA[ + +.. class:: warningmark + +**Note**: the database used must be the same as the one used in the original Kraken run + +----- + +**What is Does** + +Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple expreriments, conditions, locations, etc. It support sthe following parameters:: + + --show-zeros Display taxa even if they lack a read in any sample + --header-line Display a header line indicating sample IDs + (sample IDs are the filenames) + +----- + +**Output** + +The output of kraken-mpa-report is tab-delimited, with one line per taxon. + + + + + + ]]> + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/kraken-report.xml Thu Jul 23 10:56:14 2015 -0400 @@ -0,0 +1,49 @@ +<tool id="kraken-report" name="Kraken-report" version="1.1.0"> + <description> + view a sample report of your classification + </description> + <macros> + <import>macros.xml</import> + </macros> + <command> + <![CDATA[ + @SET_DATABASE_PATH@ && + kraken-report @INPUT_DATABASE@ "${kraken_output}" > "$output_report" + ]]> + </command> + <inputs> + <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/> + <expand macro="input_database" /> + </inputs> + <outputs> + <data format="tabular" name="output_report" /> + </outputs> + <help> +<![CDATA[ + +.. class:: warningmark + +**Note**: the database used must be the same as the one used in the original Kraken run + +----- + +**Output** + +The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows:: + + 1. Percentage of reads covered by the clade rooted at this taxon + 2. Number of reads covered by the clade rooted at this taxon + 3. Number of reads assigned directly to this taxon + 4. A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply filled with a dash. + 5. NCBI taxonomy ID + 6. Indented scientific name + +The scientific names are indented using spaces, according to the tree +structure specified by the taxonomy. + ]]> + </help> + <expand macro="version_command" /> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jul 23 10:56:14 2015 -0400 @@ -0,0 +1,30 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.10.5">kraken</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code description="Tool exception" level="fatal" range="1:" /> + </stdio> + </xml> + <xml name="version_command"> + <version_command>export LC_ALL=C && kraken --version</version_command> + </xml> + <xml name="input_database"> + <param label="Select a Kraken database" name="kraken_database" type="select"> + <options from_data_table="kraken_databases"> + <validator message="No databases are available built-in" type="no_options" /> + </options> + </param> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/gb-2014-15-3-r46</citation> + </citations> + </xml> + <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token> + <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jul 23 10:56:14 2015 -0400 @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of Kraken database in the required format --> + <table name="kraken_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/kraken_databases.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jul 23 10:56:14 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="kraken" version="0.10.5"> + <repository changeset_revision="89a36b0f718c" name="package_kraken_0_10_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>